Trunk or Treat is, in my experience, about making sure that kids are safe and about reducing the amount of walking that little kids have to do in rural areas. If he/she really wants to make halloween cupcakes, trunk or treat would actually be one of the few places where they might be accepted, assuming that he/she actually knows a few people who attend the church.
We do both - and the church has no problem with the usual array of costumes, nor is it particularly religious, save for a blessing before the kids hit the parking lot.
Between trunk/trick or treat I'd say we give out candy to between 300 and 400 kids. After the kids hit the cars, the church has a party in the rec center with baked goods and assorted drinks. That would be the place to bring the cupcakes.